Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan.
Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
Nucleic Acids Res. 2018 Jul 2;46(W1):W43-W48. doi: 10.1093/nar/gky277.
pirScan is a web-based tool for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. The purpose of our tool is to allow C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable. pirScan fulfills this purpose by first enumerating the predicted piRNA-targeting sites present in an input sequence. This prediction can be exported in a tabular or graphical format. Subsequently, pirScan suggests silent mutations that can be introduced to the input sequence that would allow the modified transgene to avoid piRNA targeting. The user can customize the piRNA targeting stringency and the silent mutations that he/she wants to introduce into the sequence. The modified sequences can be re-submitted to be certain that any previously present piRNA-targeting sites are now absent and no new piRNA-targeting sites are accidentally generated. This revised sequence can finally be downloaded as a text file and/or visualized in a graphical format. pirScan is freely available for academic use at http://cosbi4.ee.ncku.edu.tw/pirScan/.
pirScan 是一个基于网络的工具，用于在给定的 mRNA 或剪接 DNA 序列中识别秀丽隐杆线虫 piRNA 靶向位点。我们的工具的目的是允许秀丽隐杆线虫研究人员预测 piRNA 靶向位点，并避免转基因的持续生殖系沉默，这使得许多构建体无法使用。pirScan 通过首先枚举输入序列中存在的预测 piRNA 靶向位点来实现这一目的。此预测可以以表格或图形格式导出。随后，pirScan 建议可以引入输入序列的沉默突变，从而使修饰的转基因能够避免 piRNA 靶向。用户可以自定义 piRNA 靶向的严格程度以及他/她要引入序列的沉默突变。可以重新提交修改后的序列，以确保以前存在的 piRNA 靶向位点现在不存在，并且不会意外生成新的 piRNA 靶向位点。最后，可以将修订后的序列下载为文本文件，并/或以图形格式可视化。pirScan 可在 http://cosbi4.ee.ncku.edu.tw/pirScan/ 上免费供学术使用。
